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Multi-Enzyme Systems in Flow Chemistry

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Multi-Enzyme Systems in Flow Chemistry processes Review Multi-Enzyme Systems in Flow Chemistry Pedro Fernandes 1,2,3,4,* and Carla C. C. R. de Carvalho 3,4,* 1 Faculty of Engineering, Universidade Lusófona, 1749-024 Lisboa, Portugal 2 DREAMS, Universidade Lusófona, 1749-024 Lisboa, Portugal 3 Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal 4 iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal * Correspondence: [email protected] (P.F.); [email protected] (C.C.C.R.d.C.) Abstract: Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. The present review aims to present recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The types of reactors used are briefly addressed. Immobilization methodologies and strategies for the application of the immobilized biocatalysts are presented and discussed. Key aspects related to the use of whole cells in flow chemistry are presented. The combination of chemocatalysis and biocatalysis is also addressed and relevant aspects are highlighted. Challenges faced in the transition from microscale to industrial scale are presented and discussed. Keywords: microreactor; reaction cascade; whole cell; immobilization; scale-up Citation: Fernandes, P.; de Carvalho, C.C.C.R. Multi-Enzyme Systems in Flow Chemistry. Processes 2021, 9, 225. https://doi.org/10.3390/ 1. Introduction pr9020225 Flow bioreactors present large surface-to-volume ratio that is advantageous in enzy- matic reactions, but parameters such as fluid velocity which affect residence time, influence Academic Editor: significantly enzyme kinetics. Nevertheless, they provide the ability to use cascades of Gurutze Arzamendi bioreactors, each containing a different enzyme operating at its best condition, for the Received: 31 December 2020 synthesis of compounds requiring multi-steps [1–3]. Immobilization of the enzymes on Accepted: 22 January 2021 Published: 25 January 2021 the walls of the reactors or in carriers allows their reuse or continuous use, and simplifies downstream processing as the enzymes will be retained inside the reactor [4]. Publisher’s Note: MDPI stays neutral The application of whole cells in flow reactors allows multi-enzyme reactions to be with regard to jurisdictional claims in carry out with natural cofactor regeneration, usually with high region- and stereo-selectivity, published maps and institutional affil- at lower costs than if pure enzymes were used since no purification steps are required [5–7]. iations. The use of the natural ability of the cells to form biofilms on surfaces and to live in extreme environments has been used to naturally immobilize the cells on the walls of the reactors and to perform the reactions in the presence of e.g., organic solvents [8,9]. Synthetic biology and metabolic engineering tools have resulted in the production of compounds by new synthetic routes [10,11]. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. When compared to batch processes, flow systems have putatively the potential to This article is an open access article accelerate biotransformations by favoring mass transfer and to facilitate large-scale produc- distributed under the terms and tion, as smaller bioreactors and shorter reaction times are possible [12]. Both bioprocess conditions of the Creative Commons intensification and simple numbering up of bioreactors are possible, which facilitates Attribution (CC BY) license (https:// scale-up [13]. creativecommons.org/licenses/by/ In this review, we discuss the achievements and bottlenecks of multi-enzyme systems 4.0/). in flow chemistry. Processes 2021, 9, 225. https://doi.org/10.3390/pr9020225 https://www.mdpi.com/journal/processes Processes 2021, 9, 225 2 of 26 2. Flow Bioreactors The concept of flow chemistry revolves around continuously pumping fluid(s) contain- ing the starting material(s) through a reactor in a continuous manner to produce a stream of product. The reactors can be fabricated from glass, polymeric materials (e.g., polydimethyl- siloxane (PDMS), polymethyl methacrylate (PMMA), polystyrene (PS), perfluoroalkoxy (PFA)) and metal (e.g., stainless steel) or ceramics, the two later chosen when the reaction is performed under high temperature/pressure [14,15]. Depending on the volumetry and one characteristic dimension, reactors can be classified as microreactors (or microfluidic) reactors, mesoreactors and macroreactors (Table1). Table 1. Typical metrics of micro-, meso- and macroreactors. Microreactors Mesoreactors Macroreactors At least one dimension At least one dimension between 500 µm and a Dimensions above mm scale between 10 µm and 500 µm few mm Specific area 1 up to Specific area up to Specific area around 100 and 50,000 m2/m3 50,000 m2/m3 1000 m2/m3 µL range mL range L to kL range mg to g scale multi-g to kg scale kg to ton scale 1 Specific area: surface to volume ratio of the reactor. Given these respective features, microreactors display high mass and heat transfer and allow operation in laminar flow, where all the particles in the fluid move in parallel layers, with no mixing between layers, opposite to turbulent flow, where the particles in the fluid move in a random and chaotic manner. However, they have poor throughput, processing solids is challenging and they are prone to channel blockage and high pressure drops; on the other hand, mesoreactors have higher throughput and are less sensitive to pressure drops, although mass and heat transfer is less effective than in microreactors and operation in laminar flow may not be feasible. Macroreactors abridge those reactors that display volumes above a few mL [12,16,17]. Different types of reactors are used, but they can be grouped in four different types: tubular reactors, packed-bed reactors, monolith reactors and chip-based reactors [14,18]. Tubular reactors are the simplest of all: fluid flows through the channel with negligible backpressure, and hydrodynamics and heat transfer are easy to control. In tubular reactors the inner wall of the vessel is used as the carrier for enzyme immobilization (wall-coated reactors). Even for capillary-sized vessels, the surface area to volume ratio is smaller than for other microreactors; hence enzyme loading is poorer with a negative impact on the reaction efficiency. Several strategies have been suggested to improve enzyme loading, mostly involving the deposition of nanomaterials on the inner cell wall of the reactor, as recently reviewed [19]. An inner diameter of capillary as small as possible is also advised to minimize diffusion path [18,19]. Wall-coated reactors were used in cascade reactions, such as the two-step conversion of bis(p-nitrophenol)phosphate monosodium salt into p-nitrophenoxide and inorganic phosphate [20,21], and three-step production of resorufin from lactose [21]. In the later case, the coated-wall microreactor was outperformed by an equivalent packed-bed reactor based on the calculated specific substrate conversion efficiency [21]. Packed-bed reactors contain the immobilizing support and are designed in order to maximize enzyme loading. Hence, enzymes are immobilized on, e.g., hydrogels or inorganic particles that are then packed in a channel. Unlike conventional, macroscale packed-bed reactors, where mm size particles are used with negative impact in heat and mass transfer, in microreactors the particle size should be under 50 nm. The high sur- face area to volume ratio also results in shorter diffusion paths when compared with coated-wall reactors. Still, relatively high backpressure is required to achieve the in- Processes 2021, 9, 225 3 of 26 tended flow rate [14,19]. The production of (1S,2S)-1-phenylpropane-1,2-diol through an enzymatic cascade involving fusion enzymes benzoylformate decarboxylase and alco- hol dehydrogenase separately immobilize on HaloLinkTM resin. The sequential packed beds were operated for several weeks with high conversion, stereoselectivity and space– time yields up to 1850 g L−1 day−1 [22]. Pyrroline-5-carboxylate reductase and lysine-6- dehydrogenase were co-immobilized in agarose microbeads and applied in a packed-bed reactor for the continuous synthesis of L-pipecolic acid from L-lysine. Almost quantita- tive molar conversion was achieved in 30 min residence time with a space–time yield up to 2.5 g L−1 h−1 [23]. Ethyl esters were produced using combi-CLEAS of lipases from different sources. The optimized formulation was applied in a packed-bed reactor and operated for 30 days with constant conversion yields of ~50% and an average produc- −1 −1 tivity of 1.94 gethyl esters gsubstrate h [24]. Tyrosinase and DOPA-decarboxylase were immobilized in functionalized silica beads. The formulations were applied in sequential packed-bed reactors for the production of dopamine from tyrosine to achieve an overall yield of 30% [25]. Despite of their high enzyme loading capacity, packed-bed reactors still display some drawbacks, e.g., high pressure drops, limited heat transfer and risk of leakage at high flow rates. To overcome these, monolith reactors were developed that display a network of meso- or microporous structures, hence high void volume easing fluid flow and lower pressure drop. Moreover, the synthesis of monoliths is performed within the channel, thus packing procedures are avoided, although the preparation can be time-consuming and reproducibility is questionable. Monoliths can be silica- or polymeric-based; the former endure organic solvents, but are sensitive to extreme pH whereas the later are not affected by pH, but their pore structure may be affected by organic solvents [14,18,19].
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